r-cran-qtl →
1.33-7-1 →
armhf → 2014-09-01 04:26:43
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-cran-qtl 1.33-7-1 (armhf) 01 Sep 2014 04:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-cran-qtl
Version: 1.33-7-1
Source Version: 1.33-7-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-cran-qtl-Nsz_IP/r-cran-qtl-1.33-7' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-cran-qtl-Nsz_IP' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-caebd2e5-712d-400e-9493-03d8a324ac54' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7507 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8576 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 16.1 MB in 29s (551 kB/s)
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
─────────
Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'r-cran-qtl' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-qtl/trunk/
Need to get 4302 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-cran-qtl 1.33-7-1 (dsc) [2040 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-cran-qtl 1.33-7-1 (tar) [4294 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-cran-qtl 1.33-7-1 (diff) [5776 B]
Fetched 4302 kB in 0s (4403 kB/s)
Download complete and in download only mode
Check arch
──────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-NQDNi7/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
init-system-helpers
Use 'apt-get autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 25 not upgraded.
Need to get 0 B/812 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11236 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, r-base-dev
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, r-base-dev
dpkg-deb: building package `sbuild-build-depends-r-cran-qtl-dummy' in `/«BUILDDIR»/resolver-M8l7vA/apt_archive/sbuild-build-depends-r-cran-qtl-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install r-cran-qtl build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
init-system-helpers
Use 'apt-get autoremove' to remove it.
The following extra packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.9 groff-base
intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2
libcroco3 libdatrie1 libexpat1 libffi6 libfontconfig1 libfreetype6
libgfortran-4.9-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-dev
libreadline-dev libreadline6-dev libsm6 libtcl8.5 libthai-data libthai0
libtiff5 libtinfo-dev libtk8.5 libunistring0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6
libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1 libxss1 libxt6
libxxf86vm1 man-db po-debconf r-base-core r-base-dev ucf unzip x11-common
xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc
gfortran-doc gfortran-4.9-doc libgfortran3-dbg groff liblzma-doc ncurses-doc
readline-doc tcl8.5 tk8.5 less www-browser libmail-box-perl r-doc-info
r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
bzip2-doc libgl1-mesa-dri libglib2.0-data shared-mime-info xml-core
libmail-sendmail-perl r-recommended r-doc-html libfile-mimeinfo-perl
libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.9 groff-base
intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2
libcroco3 libdatrie1 libexpat1 libffi6 libfontconfig1 libfreetype6
libgfortran-4.9-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-dev
libreadline-dev libreadline6-dev libsm6 libtcl8.5 libthai-data libthai0
libtiff5 libtinfo-dev libtk8.5 libunistring0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6
libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1 libxss1 libxt6
libxxf86vm1 man-db po-debconf r-base-core r-base-dev
sbuild-build-depends-r-cran-qtl-dummy ucf unzip x11-common xdg-utils zip
zlib1g-dev
0 upgraded, 94 newly installed, 0 to remove and 25 not upgraded.
Need to get 46.9 MB/46.9 MB of archives.
After this operation, 112 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-6 [962 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.19.2-1 [30.5 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.19-1 [232 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-4 [698 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.2-1.1 [398 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0030 [69.7 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-6 [273 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-6 [310 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libglapi-mesa armhf 10.2.5-1 [65.7 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.10-3 [38.1 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.6.2-3 [126 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main libx11-6 armhf 2:1.6.2-3 [656 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main libx11-xcb1 armhf 2:1.6.2-3 [163 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.10-3 [12.1 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libxcb-dri3-0 armhf 1.10-3 [10.6 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.10-3 [23.8 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libxcb-present0 armhf 1.10-3 [10.8 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libxcb-sync1 armhf 1.10-3 [13.2 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-2 [19.6 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-2 [13.9 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libxshmfence1 armhf 1.1-2 [6736 B]
Get:30 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 10.2.5-1 [137 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.6-3 [422 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.10-3 [16.0 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.10-3 [11.0 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2+rpi1 [894 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-4 [2252 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-3 [121 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.8-1 [29.1 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.9.1-4 [154 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.35-1 [461 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+7 [287 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.9-1 [51.2 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.1-3 [27.3 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d1-1 [108 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.21-1 [159 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.21-1 [43.4 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-6 [401 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.6-1 [270 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.6-1 [204 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.6-1 [194 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu3 [20.7 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.35-3 [138 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.2-1 [31.2 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libtcl8.5 armhf 8.5.15-4 [649 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libtiff5 armhf 4.0.3-9 [191 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.2-1 [48.3 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libtk8.5 armhf 8.5.15-4 [646 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.19-1 [57.7 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.19.2-1 [116 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main cdbs all 0.4.126 [75.5 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.19.2-1 [1160 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu3 [220 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140817 [814 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.9-dev armhf 4.9.1-4 [181 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main gfortran-4.9 armhf 4.9.1-4 [4507 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main gfortran armhf 4:4.9.1-1 [1288 B]
Get:74 http://172.17.0.1/private/ jessie-staging/main libblas3 armhf 1.2.20110419-7 [186 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main libblas-dev armhf 1.2.20110419-7 [201 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-7 [27.5 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main libjpeg8-dev armhf 8d1-1 [205 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main liblapack3 armhf 3.5.0-3 [1277 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main liblapack-dev armhf 3.5.0-3 [1325 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main liblzma-dev armhf 5.1.1alpha+20120614-2 [272 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20140712-2 [65.4 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20140712-2 [153 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu3 [17.0 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.35-3 [407 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:86 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.50-2 [236 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.3-8 [105 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main libreadline-dev armhf 6.3-8 [994 B]
Get:89 http://172.17.0.1/private/ jessie-staging/main zip armhf 3.0-8 [326 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main unzip armhf 6.0-12 [152 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.1 [64.6 kB]
Get:92 http://172.17.0.1/private/ jessie-staging/main r-base-core armhf 3.1.1-1 [19.5 MB]
Get:93 http://172.17.0.1/private/ jessie-staging/main r-base-dev all 3.1.1-1 [4018 B]
debconf: delaying package configuration, since apt-utils is not installed
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No schema files found: doing nothing.
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Setting up x11-common (1:7.7+7) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.9-1) ...
Setting up libjbig0:armhf (2.1-3) ...
Setting up libjpeg8:armhf (8d1-1) ...
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Setting up fontconfig (2.11.0-6) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.36.6-1) ...
Setting up libpangoft2-1.0-0:armhf (1.36.6-1) ...
Setting up libpangocairo-1.0-0:armhf (1.36.6-1) ...
Setting up libpaper1:armhf (1.1.24+nmu3) ...
Creating config file /etc/papersize with new version
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Setting up libtcl8.5:armhf (8.5.15-4) ...
Setting up libtiff5:armhf (4.0.3-9) ...
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Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libtk8.5:armhf (8.5.15-4) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
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Setting up file (1:5.19-1) ...
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Setting up intltool-debian (0.35.0+20060710.1) ...
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:armhf (1.0.6-7) ...
Setting up libjpeg8-dev:armhf (8d1-1) ...
Setting up liblapack3 (3.5.0-3) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-3) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up liblzma-dev:armhf (5.1.1alpha+20120614-2) ...
Setting up libtinfo-dev:armhf (5.9+20140712-2) ...
Setting up libncurses5-dev:armhf (5.9+20140712-2) ...
Setting up libpaper-utils (1.1.24+nmu3) ...
Setting up libpcre3-dev:armhf (1:8.35-3) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Setting up libpng12-dev:armhf (1.2.50-2) ...
Setting up libreadline6-dev:armhf (6.3-8) ...
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Setting up zip (3.0-8) ...
Setting up unzip (6.0-12) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.1) ...
Setting up r-base-core (3.1.1-1) ...
Creating config file /etc/R/Renviron with new version
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Processing triggers for libc-bin (2.19-7) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140727-1 dpkg-dev_1.17.10 g++-4.9_4.9.1-4 gcc-4.8_4.8.3-7 gcc-4.9_4.9.1-4 libc6-dev_2.19-7 libstdc++-4.9-dev_4.9.1-4 libstdc++6_4.9.1-4 linux-libc-dev_3.14.4-1+rpi1
Package versions: apt_1.0.6 base-files_7.5+rpi1 base-passwd_3.5.33 bash_4.3-8 binutils_2.24.51.20140727-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.6 bzip2_1.0.6-7 cdbs_0.4.126 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.1-1 cpp-4.8_4.8.3-7 cpp-4.9_4.9.1-4 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.10 dpkg-dev_1.17.10 e2fslibs_1.42.11-2 e2fsprogs_1.42.11-2 fakeroot_1.20.1-1.1 file_1:5.19-1 findutils_4.4.2-9 fontconfig_2.11.0-6 fontconfig-config_2.11.0-6 fonts-dejavu-core_2.34-1 g++_4:4.9.1-1 g++-4.9_4.9.1-4 gcc_4:4.9.1-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.3-7 gcc-4.8-base_4.8.3-7 gcc-4.9_4.9.1-4 gcc-4.9-base_4.9.1-4 gettext_0.19.2-1 gettext-base_0.19.2-1 gfortran_4:4.9.1-1 gfortran-4.9_4.9.1-4 gnupg_1.4.18-2 gpgv_1.4.18-2 grep_2.20-2 groff-base_1.22.2-6 gzip_1.6-3 hostname_3.15 init_1.21 init-system-helpers_1.21 initramfs-tools_0.115 initscripts_2.88dsf-53.3 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.3-1+rpi1 kmod_18-1 libacl1_2.2.52-1 libapt-pkg4.12_1.0.6 libasan0_4.8.3-7 libasan1_4.9.1-4 libasprintf0c2_0.19.2-1 libatomic1_4.9.1-4 libattr1_1:2.4.47-1 libaudit-common_1:2.3.7-1 libaudit1_1:2.3.7-1 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.8 libbz2-1.0_1.0.6-7 libbz2-dev_1.0.6-7 libc-bin_2.19-7 libc-dev-bin_2.19-7 libc6_2.19-7 libc6-dev_2.19-7 libcairo2_1.12.16-2+rpi1 libcap2_1:2.24-4 libcgi-pm-perl_3.65-1 libcloog-isl4_0.18.2-1 libcomerr2_1.42.11-2 libcroco3_0.6.8-3 libdatrie1_0.2.8-1 libdb5.1_5.1.29-6 libdb5.3_5.3.28-6 libdbus-1-3_1.8.6-2 libdebconfclient0_0.191 libdpkg-perl_1.17.10 libdrm2_2.4.56-1 libexpat1_2.1.0-6 libfakeroot_1.20.1-1.1 libffi6_3.1-2 libfontconfig1_2.11.0-6 libfreetype6_2.5.2-1.1 libgc1c2_1:7.2d-6.3 libgcc-4.8-dev_4.8.3-7 libgcc-4.9-dev_4.9.1-4 libgcc1_1:4.9.1-4 libgdbm3_1.8.3-13 libgfortran-4.9-dev_4.9.1-4 libgfortran3_4.9.1-4 libgl1-mesa-glx_10.2.5-1 libglapi-mesa_10.2.5-1 libglib2.0-0_2.40.0-4 libgmp10_2:6.0.0+dfsg-4+rpi1 libgomp1_4.9.1-4 libgraphite2-3_1.2.4-3 libharfbuzz0b_0.9.35-1 libice6_2:1.0.9-1 libisl10_0.12.2-2 libjbig0_2.1-3 libjpeg8_8d1-1 libjpeg8-dev_8d1-1 libklibc_2.0.3-1+rpi1 libkmod2_18-1 liblapack-dev_3.5.0-3 liblapack3_3.5.0-3 liblzma-dev_5.1.1alpha+20120614-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.19-1 libmodule-build-perl_0.420800-1 libmodule-signature-perl_0.73-1 libmount1_2.20.1-5.8 libmpc3_1.0.2-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140712-2 libncurses5-dev_5.9+20140712-2 libncursesw5_5.9+20140712-2 libpackage-constants-perl_0.04-1 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpango-1.0-0_1.36.6-1 libpangocairo-1.0-0_1.36.6-1 libpangoft2-1.0-0_1.36.6-1 libpaper-utils_1.1.24+nmu3 libpaper1_1.1.24+nmu3 libpcre3_1:8.35-3 libpcre3-dev_1:8.35-3 libpcrecpp0_1:8.35-3 libpipeline1_1.3.0-1 libpixman-1-0_0.32.6-3 libpng12-0_1.2.50-2 libpng12-dev_1.2.50-2 libpod-readme-perl_0.11-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-7 libreadline-dev_6.3-8 libreadline6_6.3-8 libreadline6-dev_6.3-8 libregexp-common-perl_2013031301-1 libselinux1_2.3-1 libsemanage-common_2.3-1 libsemanage1_2.3-1 libsepol1_2.3-1 libslang2_2.2.4-17 libsm6_2:1.2.2-1 libss2_1.42.11-2 libstdc++-4.9-dev_4.9.1-4 libstdc++6_4.9.1-4 libtcl8.5_8.5.15-4 libthai-data_0.1.21-1 libthai0_0.1.21-1 libtiff5_4.0.3-9 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20140712-2 libtinfo5_5.9+20140712-2 libtk8.5_8.5.15-4 libubsan0_4.9.1-4 libudev1_208-6 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-24 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.8 libx11-6_2:1.6.2-3 libx11-data_2:1.6.2-3 libx11-xcb1_2:1.6.2-3 libxau6_1:1.0.8-1 libxcb-dri2-0_1.10-3 libxcb-dri3-0_1.10-3 libxcb-glx0_1.10-3 libxcb-present0_1.10-3 libxcb-render0_1.10-3 libxcb-shm0_1.10-3 libxcb-sync1_1.10-3 libxcb1_1.10-3 libxdamage1_1:1.1.4-2 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-2 libxft2_2.3.2-1 libxml2_2.9.1+dfsg1-4 libxrender1_1:0.9.8-1 libxshmfence1_1.1-2 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.14.4-1+rpi1 login_1:4.2-2 lsb-base_4.1+Debian13+rpi1 make_4.0-8 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.8 multiarch-support_2.19-7 nano_2.2.6-3 ncurses-base_5.9+20140712-2 ncurses-bin_5.9+20140712-2 passwd_1:4.2-2 patch_2.7.1-6 perl_5.20.0-4 perl-base_5.20.0-4 perl-modules_5.20.0-4 plymouth_0.9.0-6 po-debconf_1.0.16+nmu3 procps_1:3.3.9-7 r-base-core_3.1.1-1 r-base-dev_3.1.1-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-cran-qtl-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53.3 sysvinit_2.88dsf-53.3 sysvinit-core_2.88dsf-53.3 sysvinit-utils_2.88dsf-53.3 tar_1.27.1-2 tzdata_2014f-1 ucf_3.0030 udev_208-6 unzip_6.0-12 util-linux_2.20.1-5.8 x11-common_1:7.7+7 xdg-utils_1.1.0~rc1+git20111210-7.1 xz-utils_5.1.1alpha+20120614-2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Aug 18 13:23:23 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-cran-qtl_1.33-7-1.dsc
dpkg-source: info: extracting r-cran-qtl in r-cran-qtl-1.33-7
dpkg-source: info: unpacking r-cran-qtl_1.33-7.orig.tar.gz
dpkg-source: info: unpacking r-cran-qtl_1.33-7-1.debian.tar.xz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-caebd2e5-712d-400e-9493-03d8a324ac54
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-cran-qtl
dpkg-buildpackage: source version 1.33-7-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-cran-qtl-1.33-7
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
debian/rules build-arch
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.1.1-1)" >> debian/r-cran-qtl.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library \
--clean . ;\
fi
* installing *source* package 'qtl' ...
** package 'qtl' successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/«PKGBUILDDIR»/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c countXO.c -o countXO.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c discan.c -o discan.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c discan_covar.c -o discan_covar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c effectscan.c -o effectscan.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fill_geno_nodblXO.c -o fill_geno_nodblXO.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c findDupMarkers_notexact.c -o findDupMarkers_notexact.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fitqtl_hk.c -o fitqtl_hk.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fitqtl_hk_binary.c -o fitqtl_hk_binary.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fitqtl_imp.c -o fitqtl_imp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fitqtl_imp_binary.c -o fitqtl_imp_binary.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c forwsel.c -o forwsel.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_4way.c -o hmm_4way.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_bc.c -o hmm_bc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_bci.c -o hmm_bci.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_bcsft.c -o hmm_bcsft.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_bgmagic16.c -o hmm_bgmagic16.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_f2.c -o hmm_f2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_f2i.c -o hmm_f2i.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_main.c -o hmm_main.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_ri4self.c -o hmm_ri4self.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_ri4sib.c -o hmm_ri4sib.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_ri8self.c -o hmm_ri8self.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_ri8sib.c -o hmm_ri8sib.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hmm_util.c -o hmm_util.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c inferFounderHap.c -o inferFounderHap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c info.c -o info.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lapackutil.c -o lapackutil.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c markerlrt.c -o markerlrt.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmaugment.cpp -o mqmaugment.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmdatatypes.cpp -o mqmdatatypes.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmeliminate.cpp -o mqmeliminate.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmmapqtl.cpp -o mqmmapqtl.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmmixture.cpp -o mqmmixture.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmprob.cpp -o mqmprob.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmregression.cpp -o mqmregression.o
g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c mqmscan.cpp -o mqmscan.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pickMarkerSubset.c -o pickMarkerSubset.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ril48_reorg.c -o ril48_reorg.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ripple.c -o ripple.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_ehk.c -o scanone_ehk.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_em.c -o scanone_em.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_em_covar.c -o scanone_em_covar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_hk.c -o scanone_hk.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_hk_binary.c -o scanone_hk_binary.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_imp.c -o scanone_imp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_mr.c -o scanone_mr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scanone_np.c -o scanone_np.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scantwo_binary_em.c -o scantwo_binary_em.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scantwo_binary_hk.c -o scantwo_binary_hk.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scantwo_em.c -o scantwo_em.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scantwo_hk.c -o scantwo_hk.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scantwo_imp.c -o scantwo_imp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scantwo_mr.c -o scantwo_mr.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c simulate.c -o simulate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c simulate_ril.c -o simulate_ril.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c stahl_mf.c -o stahl_mf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c summary_scantwo.c -o summary_scantwo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c test_bcsft.c -o test_bcsft.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c util.c -o util.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c vbscan.c -o vbscan.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c zeroin.c -o zeroin.o
g++ -shared -Wl,-z,relro -o qtl.so countXO.o discan.o discan_covar.o effectscan.o fill_geno_nodblXO.o findDupMarkers_notexact.o fitqtl_hk.o fitqtl_hk_binary.o fitqtl_imp.o fitqtl_imp_binary.o forwsel.o hmm_4way.o hmm_bc.o hmm_bci.o hmm_bcsft.o hmm_bgmagic16.o hmm_f2.o hmm_f2i.o hmm_main.o hmm_ri4self.o hmm_ri4sib.o hmm_ri8self.o hmm_ri8sib.o hmm_util.o inferFounderHap.o info.o lapackutil.o markerlrt.o mqmaugment.o mqmdatatypes.o mqmeliminate.o mqmmapqtl.o mqmmixture.o mqmprob.o mqmregression.o mqmscan.o pickMarkerSubset.o ril48_reorg.o ripple.o scanone_ehk.o scanone_em.o scanone_em_covar.o scanone_hk.o scanone_hk_binary.o scanone_imp.o scanone_mr.o scanone_np.o scantwo_binary_em.o scantwo_binary_hk.o scantwo_em.o scantwo_hk.o scantwo_imp.o scantwo_mr.o simulate.o simulate_ril.o stahl_mf.o summary_scantwo.o test_bcsft.o util.o vbscan.o zeroin.o -llapack -lblas -lgfortran -lm -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/«PKGBUILDDIR»/src'
make[1]: Entering directory '/«PKGBUILDDIR»/src'
make[1]: Leaving directory '/«PKGBUILDDIR»/src'
installing to /«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library/qtl/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qtl)
rm -vf /«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library/qtl/COPYING \
/«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library/qtl/LICENSE.txt
removed '/«PKGBUILDDIR»/debian/r-cran-qtl/usr/lib/R/site-library/qtl/LICENSE.txt'
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-cran-qtl/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-cran-qtl/usr/share/lintian/overrides/r-cran-qtl; \
fi
Adding cdbs dependencies to debian/r-cran-qtl.substvars
dh_installdirs -pr-cran-qtl
mkdir -p debian/r-cran-qtl/usr/share/doc/r-cran-qtl
mv debian/r-cran-qtl/usr/lib/R/site-library/qtl/contrib debian/r-cran-qtl/usr/share/doc/r-cran-qtl/examples
mkdir -p debian/r-cran-qtl/usr/share/doc/r-cran-qtl/tests
cp -a tests/*.R tests/*.csv tests/*.map tests/*.raw tests/*.Rout.save debian/r-cran-qtl/usr/share/doc/r-cran-qtl/tests
dh_installdocs -pr-cran-qtl
dh_installexamples -pr-cran-qtl
dh_installman -pr-cran-qtl
dh_installinfo -pr-cran-qtl
dh_installmenu -pr-cran-qtl
dh_installcron -pr-cran-qtl
dh_installinit -pr-cran-qtl
dh_installdebconf -pr-cran-qtl
dh_installemacsen -pr-cran-qtl
dh_installcatalogs -pr-cran-qtl
dh_installpam -pr-cran-qtl
dh_installlogrotate -pr-cran-qtl
dh_installlogcheck -pr-cran-qtl
dh_installchangelogs -pr-cran-qtl
dh_installudev -pr-cran-qtl
dh_lintian -pr-cran-qtl
dh_bugfiles -pr-cran-qtl
dh_install -pr-cran-qtl
dh_link -pr-cran-qtl
dh_installmime -pr-cran-qtl
dh_installgsettings -pr-cran-qtl
dh_strip -pr-cran-qtl
dh_compress -pr-cran-qtl
dh_fixperms -pr-cran-qtl
dh_makeshlibs -pr-cran-qtl
dh_installdeb -pr-cran-qtl
dh_perl -pr-cran-qtl
dh_shlibdeps -pr-cran-qtl
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-cran-qtl/usr/lib/R/site-library/qtl/libs/qtl.so was not linked against libstdc++.so.6 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-cran-qtl/usr/lib/R/site-library/qtl/libs/qtl.so was not linked against libgfortran.so.3 (it uses none of the library's symbols)
dh_gencontrol -pr-cran-qtl
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-cran-qtl
dh_builddeb -pr-cran-qtl
dpkg-deb: building package `r-cran-qtl' in `../r-cran-qtl_1.33-7-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-cran-qtl_1.33-7-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build r-cran-qtl-1.33-7
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140901-0426
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-cran-qtl_1.33-7-1_armhf.changes:
──────────────────────────────────
Format: 1.8
Date: Mon, 18 Aug 2014 15:17:44 +0200
Source: r-cran-qtl
Binary: r-cran-qtl
Architecture: armhf
Version: 1.33-7-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-cran-qtl - GNU R package for genetic marker linkage analysis
Changes:
r-cran-qtl (1.33-7-1) unstable; urgency=medium
.
* New upstream version
* Normalised source package name
Checksums-Sha1:
fb509607afac1342dd10a852e3243014ed1885b3 4370090 r-cran-qtl_1.33-7-1_armhf.deb
Checksums-Sha256:
bdcc2ca9eea967eabc4ad292ec3cd5c1bbd0aeb8ca220a8fa5cca8b903f29e98 4370090 r-cran-qtl_1.33-7-1_armhf.deb
Files:
e8d787ce276a040282f15f77f8849ed6 4370090 gnu-r optional r-cran-qtl_1.33-7-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-cran-qtl_1.33-7-1_armhf.deb
─────────────────────────────
new debian package, version 2.0.
size 4370090 bytes: control archive=6854 bytes.
1969 bytes, 37 lines control
15724 bytes, 179 lines md5sums
Package: r-cran-qtl
Version: 1.33-7-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5606
Depends: libblas3 | libblas.so.3, libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libgfortran3 (>= 4.3), liblapack3 | liblapack.so.3, libstdc++6 (>= 4.1.1), r-base-core (>= 3.1.1-1)
Suggests: r-cran-snow
Section: gnu-r
Priority: optional
Homepage: http://www.rqtl.org
Description: GNU R package for genetic marker linkage analysis
R/qtl is an extensible, interactive environment for mapping quantitative
trait loci (QTLs) in experimental crosses. It is implemented as an
add-on-package for the freely available and widely used statistical
language/software R (see http://www.r-project.org).
.
The development of this software as an add-on to R allows one to take
advantage of the basic mathematical and statistical functions, and
powerful graphics capabilities, that are provided with R. Further,
the user will benefit by the seamless integration of the QTL mapping
software into a general statistical analysis program. The goal is to
make complex QTL mapping methods widely accessible and allow users to
focus on modeling rather than computing.
.
A key component of computational methods for QTL mapping is the hidden
Markov model (HMM) technology for dealing with missing genotype data. The
main HMM algorithms, with allowance for the presence of genotyping errors,
for backcrosses, intercrosses, and phase-known four-way crosses
were implemented.
.
The current version of R/qtl includes facilities for estimating
genetic maps, identifying genotyping errors, and performing single-QTL
genome scans and two-QTL, two-dimensional genome scans, by interval
mapping (with the EM algorithm), Haley-Knott regression, and multiple
imputation. All of this may be done in the presence of covariates (such
as sex, age or treatment). One may also fit higher-order QTL models by
multiple imputation.
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Build Architecture: armhf
Build-Space: 22072
Build-Time: 249
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 370
Job: r-cran-qtl_1.33-7-1
Machine Architecture: armhf
Package: r-cran-qtl
Package-Time: 670
Source-Version: 1.33-7-1
Space: 22072
Status: successful
Version: 1.33-7-1
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Finished at 20140901-0426
Build needed 00:11:10, 22072k disc space